I'm trying to install Flagmatic on Mac OS X Yosemite, a software package used to solve problems in extremal graph theory using the "flag algebras" developed by Razborov. I'd like to use Flagmatic to help with a research problem I'm working on, but I'm finding it very difficult to install. I'm a mathematician and while I've had some experience using Sage and Python through the Terminal I don't really know how to fix the sort of problems that I'm running into here. Here's the most up-to-date user guide so you can follow what I'm trying to do. I can broadly break down the problem as follows:
First, there is a link in the user guide to download the semidefinite programming package CSDP which Flagmatic needs in order to do some calculations. You then need to move CSDP to somewhere Flagmatic can find it, so I typed
sudo cp ~/Downloads/csdp/usr/local/bin/
into Terminal, which seemed to work. Then the user guide says by typing
csdp
into Terminal it should launch CSDP. This doesn't work - I get a permission denied message even though I typed sudo. Can anyone explain why this is happening and how to remedy it?
Secondly, when I run Sage (maths software) in the Terminal, I then want to be able to change directory to the pkg folder where there is a script called setup.py. When I run sage and type
python setup.py install
or
-python setup.py install
while in the pkg directory, I get an invalid syntax message with a pointer to the particular phrase setup.py. This is what the user guide tells you to do. If I instead try to install outside of Sage I get an error message The environment variable SAGE_ROOT must be defined. Can anyone provide some explanation and help with how to fix this?
Wow, this is somewhat dated information that they provide, since for well over a year csdp is an experimental Sage package. You should be able to just do
sage -i csdp
to install it (if you have compiler tools, which you probably do in this case). I guess the old instructions would still work but are a little brittle w.r.t. Sage.
Anyway, to the actual problem. You need to do the exact command given in the instructions:
sage -python setup.py install
However, this assumes (!) that you have a sage command in your PATH. Which you may not!
In this case, I recommend you use whatever command you use to run Sage, but instead of just typing /commmand/for/sage do /command/for/sage -python setup.py install in that directory. It will have all the right environment variables set up so that it installs in the right place, I am guessing.
Now, I'm not sure why flagmatic isn't just having themselves become an upstream package on the Sage servers, but that is a question that is harder to answer.
I might udpate the documentation in the near future. For now, however, you might want to visit this: https://github.com/jsliacan/flagmatic-2.0.git. I keep Emil's copy of Flagmatic 2.0 with updated install info. If you follow the README file, you should be fine.
I just built sage on Yosemite from source (worked fine) and then installed Flagmatic 2.0 (or Flagmatic-dev) without difficulties. It should work for you too.
I hope this helps.
Related
I am currently working on a personal project using the Ruby language in Cloud9 IDE. Recently, I came across an environment/programming language called Processing. My goals is to make Processing available for my use in Cloud9 IDE.
I am a complete novice and have no clue what I am doing. I followed directions from the following website: Directions for setting up Processing
I entered the following commands into Cloud9's terminal:
rvm install jruby
rvm use jruby
gem install ruby-processing
PROCESSING_ROOT: "/Applications/Processing.app/Contents/Java"
Entering in PROCESSING_ROOT: "/Applications/Processing.app/Contents/Java"
outputted message bash: PROCESSING_ROOT:: command not found
I wasn't too surprised by this, since the last entry probably needs information specific to my setup. Here are my questions:
1.) Are these directions correct for what I am trying to do? (get Processing to work in Cloud9 IDE). If they are not correct, can someone please point me to the correct directions, or give me directions?
2.) If these directions are correct, how can I successfully finish the last step? I tried running DrawRuby.rb, a simple program copied from the internet that supposedly made use of Processing. When I ran the code, the message "You need to set PROCESSING_ROOT in ~/.rpsrc" appeared. I am not sure if this piece of information is relevant or not, but I figured I would add it.
This is where I am at, and I am completely stuck. If someone could give me some help, I would be very grateful. Also, please make your explanation easy to understand. I am relatively new to the programming world, and may not necessarily understand terminology or how things should work.
Cheers!
*** Edit: I created a new workspace in Cloud9 IDE and tried Jed's suggestion. This is what happened:echo 'PROCESSING_ROOT: "/Applications/Processing.app/Contents/Java"' > ~/.rpsrc
:~/workspace $ rp5 run Draw.rb
WARNING: you need to set PROCESSING_ROOT in ~/.rp5rc
NameError: uninitialized constant Processing::RP_CONFIG
Did you mean? Config
RbConfig
const_missing at org/jruby/RubyModule.java:3344
spin_up at /usr/local/rvm/gems/jruby-9.1.7.0/gems/ruby-processing-2.7.1/lib/ruby-processing/runner.rb:188
run at /usr/local/rvm/gems/jruby-9.1.7.0/gems/ruby-processing-2.7.1/lib/ruby-processing/runner.rb:105
execute! at /usr/local/rvm/gems/jruby-9.1.7.0/gems/ruby-processing-2.7.1/lib/ruby-processing/runner.rb:67
execute at /usr/local/rvm/gems/jruby-9.1.7.0/gems/ruby-processing-2.7.1/lib/ruby-processing/runner.rb:61
<main> at /usr/local/rvm/gems/jruby-9.1.7.0/gems/ruby-processing-2.7.1/bin/rp5:10
load at org/jruby/RubyKernel.java:979
<eval> at /usr/local/rvm/gems/jruby-9.1.7.0/bin/rp5:1
eval at org/jruby/RubyKernel.java:1000
<main> at /usr/local/rvm/gems/jruby-9.1.7.0/bin/jruby_executable_hooks:15
You need to add a file to your home directory (~/) called .rpsrc and then add that environmental setting (PROCESSING_ROOT) to your file. The following should work from the command line in your cloud9 environment:
echo 'PROCESSING_ROOT: "/Applications/Processing.app/Contents/Java"' > ~/.rpsrc
I know it might be a bit late for you but ruby-processing is now deprecated, and will only work with processing-2.2.1. For processing-3.3.7 use either JRubyArt or propane latter does not even require processing install.
I am currently attempting to install the tensorflow object detection app on Windows 7 (employer requirement) and I am failing at a few steps from the end.
Basically I get the following error when I run the installation test command:
ImportError: No module named nets.
I have read some solutions on the subject:
https://github.com/tensorflow/models/issues/729
https://github.com/tensorflow/models/issues/1842
which looks like this:
export PYTHONPATH="$PYTHONPATH:"somepath"/tensorflow/models/slim"
basically meaning that I must set the right path in the PYTHONPATH environmental variable.
Working with Windows, I tried calling this:
SET PYTHONPATH="$PYTHONPATH:C:tensorflow/models/slim
And when it didn't work, I created a PYTHONPATH variable in system-> environmental variables.
I'm still getting the error so I suppose that I am still missing something but due to my lack of knowledge I still can't figure out what.
Would someone familiar with Windows be able to point out what's missing?
Thanks
in linux:
add export export PYTHONPATH=$PYTHONPATH:pwd:pwd/slim to ~/.bashrc
attention:you should keep single quote mark
if you work with windows, i guess it should like this:PYTHONPATH=$PYTHONPATH:'C:/tensorflow/models':'C:/tensorflow/models'/slim
just my guess, you can take a try.
good luck!
If you run the setup.py it will install all the relevant modules for object detection. The other option is download the git directory. cd to the folder and try to run the module from there. You might face protubuf issue. Try to install it before running the code. It's bit complicated to install protobuf in windows. But if you are not using ".pb" file, then you don't need to.
I figured out a way to make it work. I am not writing this as a final answer as it is mostly a workaround and due to lack of understanding from my part I cannot guarantee it will work (and also it might not be best good practice).
Anyway here it is:
As Beta previously suggested, you have to run setup.py, however running it from models folder did not do it for me, I also had to run it from object detection folder.
However there was a problem there, it generated an error saying the BUILD already existed (which was correct) so I had to delete the BUILD file from inside of model.
After that it worked, turns out the path I had set was working fine.
Now if some experts would look into this and explain how and why this workaround worked it might make this a valid solution.
I wanted to install caffe on openSuse.
Just for the record - it worked out for me, I just don't know what's the "exact" way to do this. The things I did maybe aren't really for someone who's new to this, and also it was kind of a "bad installation". My way was the following:
First, I did
make all
This worked, until it complained that some libraries weren't found (libclbas etc.). So I used
ccmake .
to change the paths to the libraries manually. I needed to manually type the paths to the snappy, boost_python, blas, cblas and lapack libs. After doing that I did
cmake .
and then
make
and everything worked. My problem now is - why doesn't make find the libs, and is there a way to fix this? I think the problem was that I didn't have /usr/lib/libcblas.so but /usr/lib/libcblas.so.3, and similar "problems" with the other libraries.
Another thing - when I tried using ccmake/cmake right from the beginning (without the make part first), there weren't any files in my build directory (like $CAFFE_ROOT/build/examples or $CAFFE_ROOT/build/tools were empty), so the mnist tutorial for example wasn't working. That's why I first called
make all
, what may seem strange to you.
Of course I know how to fix this stuff, but I would like to know how the correct way for a "clean and simple installation" is. Did is miss anything when using make/cmake, is this some kind of inconsistency in caffe or something else? And, what is the clean way to do this?
Maybe look at the Ubuntu installation guide? http://caffe.berkeleyvision.org/install_apt.html
It mentions all the different packages you might need. I couldn't find openSuse installation instructions - but you should be able to translate the apt-get commands for your platform.
I am new in the world of OpenMDAO (and also on Python) and I am having some problems to understand the use of the software. I have already installed Anaconda (pyth v2.7) and the OpenMDAO, but I don't know how to run it. I am following this tutorial but I am not sure if I am doing it properly. I write the .py files in notepad++, and I try to run on the IPython but when I use the command : from paraboloid import Paraboloid it appears an error : No module named.api. I think that maybe I am not using the correct path (I'm in the folder where I have the .py files). Probably it's an stupid error, so sorry for the question.
Thank you all, Jose M O
If your tutorial link above is correct, I see that you are using a tutorial for OpenMDAO 0.1.0. That version is 5.5 years old at this time, and is no longer supported. We will be happy to help with your questions, but to get a better foundation, and a much more useful tool, please consider:
Install OpenMDAO 1.5.0 (pip install openmdao or read these installation docs)
Try this paraboloid tutorial instead.
Good luck,
Keith
NOTE: If you installed OpenMDAO 1.x.x and are using the tutorial from 0.1.0, you would have many problems with api imports, as many things have changed since 0.1.0.
I'm a total newbie in Mac OS X, R and C++. Sound like a good mix, doesn't it?
I have the need to use RQuantLib, because I want to use some pricing functions part of the QuantLib package inside R, all on a Mac OS X-powered environment.
I've correctly installed QuantLib. I've already asked to the official QuantLib mailing list, and together we seem to have reached the conclusion that the problems I'm encountering are not related to my QuantLib installation, which seems ok and correctly configured.
So, I turned to R to try and solve the problem. Whenever I try to run ZeroCouponBond from within R, copying and pasting the first example provided with the official documentation, I get the following error:
"Error in DiscountCurve.default(discountCurve.param, list(flat = 0.05)) :
cannot find function errorOccured"
Now, I would rule any syntax.related problem out, since I'm copying the very same example present in the official help.
I don't know what I did wrong, but I know I need to find a solution at all costs. I've installed Rcpp, and the configuration seems really ok. Just one question I was not able to find an answert to: in my understanding, RQuantLib basically acts as a link between QuantLib and R. If that's correct, how can I tell RQuantLib where to look to find libQuantLib.a, that is, the compiled library resulting from the "make && sudo make install" commands performed while installing QuantLib itself?
Right, so, I've finally managed to get it to work.
First of all, I would like to say that things would have been much easier if a thorough, step-by-step installation procedure had been provided. I acknowledge I'm a total newbie, but I think other people approaching to R for the first time might encounter difficulties similar to those I had to overcome.
Anyway, this is what I did:
I've downloaded the .tar.gz source packages for both Rcpp and RQuantLib from cran.r-project.org
I've compiled them installing them from within the R environment. This is where I was making a mistake. Indeed, I was trying to compile them by invoking the configure installation script from the terminal; however, as Dirk said, the config script looks for QuantLib's quantlib-config script, and I didn't know the correct syntax to tell the configure script the correct path to QuantLib. Executing the procedure from R (by just installing the package) sorts out any problem, as all the dependencies are correctly located and loaded
So, that's pretty much it: just install the .tar.gz source package as you would do with the binary version, and everything should work ok.
Of course, I'm still curious to understand:
If it is possible to compile Rcpp and RQuantLib from the terminal; and
Why the binary version for Mac OS X will not work on my system, ie: why do I have to compile starting from the source code?
Thank you so much to anyone willing to answer my (probably naive and silly) questions. I'm eager to understand a bit more!
Thanks!
The RQuantLib package uses a tool called configure which determines the patch at package build-time. It looks for the script quantlib-config from which it learns about the location of libQuantLib.a.
First, install boost (brew install boost) and, secondly, Quantlib (currently at 1.7.1) by following instructions at http://quantlib.org/install/macosx.shtml:
cd QuantLib-1.x.y
./configure --enable-static --with-boost-include=/opt/local/include/ \
--with-boost-lib=/opt/local/lib/ --prefix=/opt/local/
make && sudo make install
It takes some time (~1 hour) for make.
Then in R or Rstudio, install packages Rcpp and RQuantlib. The later requires type="source" since only source package is available.
At this point, you should be able to use RQuantlib. The American Option value (SPY as of 4/1/2016, maturity 7/15/2016) can be calculated in R as
AmericanOption("put", strike=206, volatility=0.1525, underlying = 206.92, 0.021, 0.003, 73/252, engine="CrankNicolson")